NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes

Microbial-algal symbiotic system drives reconstruction of nitrogen, phosphorus, and methane cycles for purification of pollutants in aquaculture water

Intensive aquaculture's excessive nitrogen, phosphorus, and methane emissions caused environmental degradation. This study explored how algae-bacteria symbiotic systems (ABSS) enhanced water purification by regulating element cycles. We established a Chlorella pyrenoidosa-Bacillus subtilis symbiotic system. At a 1:1 bacteria-to-algae ratio, chlorophyll a and cell dry weight were highest. C. pyrenoidosa supplied organic acids, carbohydrates, and amino acids to B. subtilis, which reciprocated with amino acids, purines, and vitamins. ABSS significantly reduced total nitrogen, ammonia nitrogen (NH4+-N), nitrite (NO2--N), nitrate (NO3--N), phosphate (PO43--P), total phosphorous, dissolved organic carbon, and chemical oxygen demand in aquaculture water. It reshaped microbial communities and enriched key genus (Limnohabitans, Planktophila, Polaromonas, Methylocystis) and upregulating genes linked to organic phosphate mineralization, methane oxidation, and nitrate reduction. These changes strengthened nitrogen-phosphorus-methane cycle coupling, boosting water purification. ABSS offers an eco-engineering solution for aquaculture pollution by optimizing microbial interactions and nutrient cycling.

Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment

The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.

Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake

Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.

The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments

Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.

Coupled nitrogen and phosphorus cycles mediated by coordinated variations of functional microbes in industrial recirculating aquaculture system

Industrial Recirculating Aquaculture Systems (IRAS) represent a sustainable and efficient approach to aquaculture, offering significant benefits in water conservation and environmental management. A comprehensive understanding of nitrogen (N) and phosphorus (P) cycling is essential for optimizing system design and operational strategies, enabling the maintenance of a balanced ecosystem within IRAS. Here, water microbial communities in the shrimp aquaculture pond (AP) and nitrification tank (NT) of the IRAS were investigated using a metagenomics-based approach to explore the mechanisms of N and P coupling cycles. Results showed that (1) N and P cycling genes were more abundant in AP water than in NT, with higher potentials for degrading organic N and P compounds, nitrate reduction, denitrification, and phosphate uptake in AP; and their hosts (functional bacteria) were identified as Marivivens for nitrate reduction, Polaribacter and Erythobacter for organophosphorus hydrolysis, and Fluviibacter and Sediminibacterium for phosphate uptake; (2) the coupling of N and P cycles was observed through the abundance of functional genes, likely mediated by coordinated variations in host composition, with nitrite content as a key factor influencing this variation; several bacterial species possessing both N and P cycling genes were identified, primarily engaged in the degradation of organic N and P compounds, denitrification, and phosphate uptake. This study highlights the coupling of N and P cycling in IRAS and the important role of functional bacteria in maintaining water quality. The results also have important implications for the management and improvement of IRAS for more effective aquaculture activities.

The control of physical and biological drivers on pelagic methane fluxes in a Patagonian fjord (Golfo Almirante Montt, Chile)

Methane fluxes from coastal waters such as fjords and the underlying control mechanisms are poorly understood. During the austral summer, we investigated a fjord in the Chilean part of Patagonia, the Golfo Almirante Montt. The study is based on measurements of methane concentration, stable carbon isotopes and the distribution and activity of methane-oxidizing bacteria in the water column, as well as oceanographic and geological observations. Our results indicate that methane is of biogenic origin and released from gas-rich sediments at the entrance of the fjord, characterized by pockmarks and gas flares. Tidal currents and turbulent mixing at the sill cause a near-surface methane plume to spread into the main fjord basin and mix with the methane- and oxygen-depleted deep water. Wind-induced mixing at the sea surface controls the methane flux from the plume into the atmosphere. The methane plume is consumed by methanotrophic bacteria of the Methylomonadaceae and Ga0077536 families, which are differently distributed along the water column. An enrichment of the characteristic gene methane monooxygenase (pmoA) in the methane-poor deep water, and a conspicuously high δ13C-CH4 signature suggest that methane-rich intrusions regularly enter the deep water, where the methane is microbially oxidized. Our interdisciplinary study offers a comprehensive insight into the complex physical and biological processes that modulate methane dynamics in fjords and thus help to better assess how methane emissions from these systems will change under anthropogenic influence.

Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments

Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.

Active restoration facilitates sedge colonization in degraded alpine meadows on the Qinghai-Tibetan Plateau

Extremely degraded alpine meadow is among the most challenging types of grasslands to restore due to its severely deteriorated habitat and limited self-recovery capability. Since the 2000s, cultivating artificial grasslands has been widely applied as the primary method for restoring theses meadows on the Qinghai-Tibetan Plateau (QTP). However, the performance of climax species (sedges of alpine meadows on the QTP), which is crucial to determine the restoration efforts of alpine meadow, has not received sufficient attention yet. With this context, field data of cultivated grasslands with different restoration stages (S1: 1-6 years, S2: 7-12 years, S3: over 13 years), was collected to examine the change and influencing factors of sedges over restoration time. The results demonstrated that restoration actions facilitated increases in the sedge biomass and the percentage of sedge biomass in S3, though these values remained lower than those in healthy alpine meadow. A clear difference in plant community structure was observed among different grasslands, characterized by an increase in forb abundance and species richness alongside a decrease in grass abundance over restoration time. Soil moisture and organic carbon of S2 and S3, and soil total nitrogen of S3 were significantly improved, while soil available nutrients remained stable compared to the degraded meadow. The relative abundance of most nitrogen- and phosphorus-related functional genes either declined or stabilized during the restoration process. The sedge biomass (77.36 %) and the percentage of sedge biomass (88.35 %) were largely explained by the coupling effects of plant indicators (grass abundance and species richness) and soil indicators (soil bulk density, moisture, organic carbon, and total nitrogen). This study highlights the positive influence of active restoration actions on sedge colonization and the asynchronous dynamics between aboveground (plant community) and belowground components (soil available nutrients and microbial community). These findings imply that accelerating soil nutrients accumulation and cycling should be prioritized in post-restoration management of cultivated grasslands on the QTP and other alpine regions.

The Competitive/Cooperative Dynamics of Sulfur Disproportionation Microbes and Methanogens in Geogenic High-Iodine Groundwater Systems

The microbial transformation of iodine-bearing organic matter (OM) and iron (Fe) minerals is a critical process that controls the release of iodine (I) to groundwater. However, the roles of functional microbial types, OM molecular characteristics, and microbe-OM interactions in iodine mobilization remain unclear. In this study, groundwater samples with different iodine concentrations were collected from the central Yangtze River basins, China. Using 16S rRNA gene sequencing, we identified sulfur disproportionation and methanogenesis as dominant metabolic processes in relatively low-I (<300 μg/L) and high-I (>300 μg/L) groundwater, respectively. Sediment incubation experiments showed that combined sulfur disproportionation and methanogenesis can promote iodine release by 87.1%. Ultrahigh-resolution molecular characterization of the organic components revealed that sulfur-disproportionating microbes may selectively metabolize bioactive OM (e.g., aliphatic compounds and oxygen-poor highly unsaturated compounds), leaving recalcitrant OM (e.g., N-containing oxygen-rich highly unsaturated compounds, polyphenols, and polycyclic aromatic compounds) in groundwater, and methanogenic microbes preferentially consume bioactive OM in low-I groundwater and recalcitrant OM in high-I groundwater. Thus, a cooperative-competitive pattern between methanogens and sulfur disproportionating microorganisms may influence OM degradation and potentially contribute to iodine mobilization. This study highlights that the OM transformation process, driven by biological sulfur disproportionation and methanogenesis, promotes iodine enrichment in alluvial-lacustrine groundwater and improves our understanding of the genesis of geogenic high-iodine groundwater systems.

Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai-Tibetan Plateau

Alpine meadows on the Qinghai-Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows.

Integrating network and in-silico simulation insights into the ecological interactions shaped by carbon sources in partial denitrification and anammox system

The underlying ecological mechanism of microbial communities shaped by carbon source in partial denitrification and anammox (PDA) systems remains poorly understood, despite the potential of multiple carbon sources to support the partial denitrification process. Herein, the integrated network and in-silico simulation methods were used to evaluate the considerable impact of carbon sources on the dynamics of ecological interactions. The fluctuation of carbon source (from acetate to glucose and ethanol) significantly destabilized the performance of PDA system (total nitrogen removal efficiency decreased from 96.8% to 69.1%). Glucose simultaneously altered the composition of denitrifying bacteria, resulting in a significant enrichment of the genus Elstera (from 0% to 12.7%). By contrast, genus Thauera re-dominated for partial denitrification with ethanol as carbon source. Importantly, heterotrophic bacteria (e.g., genus Calditrichia) gradually enriched by utilizing ethanol. The presence of acetate in phase IV further enhanced the competitive advantage of heterotrophic bacteria over denitrifying bacteria, thereby resulting in the deteriorated performance of the PDA system. The in-silico simulation of co-culture further revealed that the overgrowth of auxotrophic species Calditrichia utilized amounts of nutrients and limited other functional bacteria. Additionally, the whole co-occurrence network indicated that positive interactions likely improved the adaptability of anammox bacteria under the unsteady conditions. This study provides profound insights into the ecological interactions shaped by carbon sources in PDA systems and underscores the necessity of comprehensive review of the external carbon source to ensure optimal performance.

Livestock-Crop-Mushroom (LCM) Circular System: An Eco-Friendly Approach for Enhancing Plant Performance and Mitigating Microbiological Risks

Mushroom production using agroforestry biowaste is a great green cycling agriculture alternative. Therefore, the current study explored the Livestock-Crop-Mushroom (LCM) circular production model, starting with co-composting of straw and cow manure as a'St' biofertilizer further used for mushroom cultivation that ultimately produced a'StM' biofertilizer. The two biofertilizers were tested for their impacts on plant growth and potential microbial risks. The results show significant growth of oats stimulated by biofertiliser use. Both'St' and'StM' increased plant biomass, while with the latter, the crude protein content (+5.1%) and root biomass were also higher. Reduced abundances of resistome genes (30%) and pathogens (25%) were observed during the oat growth. Further, metagenomics analysis also indicated a reduction in antibiotic-resistance genes by -20% in soils with oats treated by'St' and -46% in'StM' biofertilizer treatment. The'StM' had a three-fold stronger inhibitory effect on oat rhizosphere soil pathogens than'St'. Moreover, compared to'St','StM' suppressed pathogens in seeds and stems, with specific beneficial biomarker microbes in different plant parts. Overall, the antibiotic resistance gene related to oxytetracycline decreased more than three-fold in the LCM system. This study demonstrates the substantial potential and scalability of the LCM circular system within the agricultural domain.

Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation

The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.

Multi-omics analysis to a sludge composting system reveals thermophilic bacteria promote free amino acid production and compost quality

Recycling waste nutrients from waste activated sludge (WAS) back to agricultural land through composting embodies the core principle of circular economy. However, large quantities of nitrogen are lost as nitrogenous gases during composting, reducing the fertilization performance of the final products. Here, the N cycle and amino acid (AA) biotransformation profiles in an industrial-scale sludge composting plant (130t/d) were investigated using replicated and temporally sampled multi-omics datasets. The results revealed that 44.4 % of nitrogen was lost to nitrogenous gas after composting, and the enhanced N cycle - specifically, (i) glutamate → NH3 +α-ketoglutarate, (ii) glutamate + NH3→ glutamine, and (iii) glutamine + aspartate → asparagine + glutamate, mainly mediated by thermophilic Pseudoxanthomonas. sp, are responsible for nitrogen loss. During thermophilic stage, 71.4 % of enzymes involved in AA transformation were upregulated, leading to a peak free AA content of 10.60 mg/g-TS, with glutamate comprising 51.8 % of the total. When composting reached cooling stage, free AA content dropped quickly to 5.74 mg/g-TS. Based on nitrogen monitoring and AA-centered transformation, a novel short-term composting strategy was proposed for AA-rich compost production. Then, plant experiments demonstrated that AA-rich compost outperformed conventional compost in promoting plant growth under both pot and hydroponic conditions, likely by improving root amino acid transport. Sustainability analysis revealed that the total cost and greenhouse gas emissions of AA-rich compost production were 31.9 % and 74.9 % lower than those of conventional compost, respectively. These findings provide a potential solution to make WAS more sustainable by regulating free AA production.

Dissimilatory nitrate reduction pathways drive high nitrous oxide emissions and nitrogen retention under the flash drought in the largest freshwater lake in China

Flash drought (FD) events induced by climate change may disrupt the normal hydrological regimes of floodplain lakes and affect the plant-microbe mediated dissimilatory nitrate reduction (DNR), i.e., denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA), thus having important consequences for nitrous oxide (N2O) emissions and nitrogen (N) retention. However, the responses of the DNR pathways in the floodplain lake to the record-breaking FD in 2022 in Yangtze River of China, as well as the underlying microbial mechanisms and feedbacks to climate change remain poorly understood. Here, we collected exposed sediments and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during 2022 FD and the dry seasons prior to and after this event. The potential DNR rates and the synergistic metabolism of microbial guilds involved in DNR were investigated using 15N isotope pairing technique, high-throughput and metagenomic sequencing. We found that the in situ N2O fluxes in the littoral wetlands were highest during the flash drought, especially in the exposed sediments. The potential DNRA rates were highest under flash drought conditions, and DNRA dominated the DNR for both exposed sediments (80.4 %) and Carex cinerascens-associated soils (57.5 %). Nutrients (i.e., N and P) and DNRA bacterial communities played a key role in producing the extremely high N2O fluxes from exposed sediments, which could be explained by the synergistic metabolism of DNRA bacteria and denitrifiers through the exchange of the key intermediates in DNR. Therefore, the climate change-induced flash drought promoted greater nitrous oxide emissions and N retention in the littoral wetlands of Poyang Lake, producing a greater flux of greenhouse gas emissions and elevating the risk of lake eutrophication. Hence, flash droughts reinforce a positive feedback between climate change and nitrous oxide emission from these aquatic ecosystems.

Transcriptome analysis of nitrogen assimilation preferences in Burkholderia sp. M6-3 and Arthrobacter sp. M7-15

Introduction

Ammonium (NH4 +) and nitrate (NO3 -) are the two main forms of inorganic nitrogen (N) that exist in soil and both can be absorbed and utilized by plants. As a vast and crucial biome, soil microorganisms are responsible for mediating the inorganic N assimilation process and enhancing nitrogen use efficiency. Understanding how these microorganisms assimilate different forms of inorganic nitrogen is crucial. There are a handful of microorganisms that play a dominant role in the process of soil inorganic nitrogen assimilation and have a significant advantage in abundance. However, microbial preferences for ammonium or nitrate, as well as differences in their metabolic pathways under co-existing ammonium and nitrate conditions, remain unclear.

Methods

In this study, two microbial strains with nitrogen assimilation advantages, Burkholderia sp. M6-3 and Arthrobacter sp. M7-15 were isolated from an acidic Chinese soil and then incubated by different sources of inorganic N to investigate their N preferences. Furthermore, RNA sequencing-based transcriptome analysis was used to map the metabolic pathways of the two strains and explore their explanatory potential for N preferences.

Results

The results showed that strain M6-3 preferred to utilize NH4 + while strain M7-15 preferred to utilize NO3 -. Although both strains shared similar nitrogen metabolic pathways, the differential expression of the glutamine synthetase-coding gene glnA played a crucial role in regulating their inorganic N preferences. This inconsistency in glnA expression may be attributed to GlnR, a global regulator of nitrogen utilization.

Discussion

This research strengthens the theoretical basis for exploring the underlying causes of differential preferences for inorganic N forms and provided key clues for screening functional microorganisms to ultimately enhance inorganic nitrogen use efficiency.

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.

Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets

In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.

Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.

Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation

Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.

Impact of adaptation time on lincomycin removal in riverbank filtration: A long-term sand column study

Riverbank filtration (RBF) is an effective pretreatment technology for drinking water, removing organic micropollutants (OMPs) mainly through biodegradation. Despite documented improvements in OMP removal with extended adaptation time, the mechanisms remain poorly understood. This study assessed the removal of 128 OMPs over 82 d in a simulated RBF system, identified those with improved removal, and analyzed their properties. Additionally, microbial community shifts after 400 d of lincomycin exposure were studied to understand the underlying mechanisms. We found that the removal efficiencies of 24 OMPs, including lincomycin and fluconazole, improved by 3-77 % over 82 d while being positively correlated with the presence of tertiary amides and secondary sulfonamides. Lincomycin removal efficiency rose from 20 % to 95 % over 68 days and stayed high. We identified eight potential degradation products of lincomycin, occurring primarily via hydroxylation, N-demethylation, and amide hydrolysis. Additionally, lincomycin notably increased the abundances of specific antibiotic-resistant bacteria (e.g., Thiobacillus, 8.3-fold) and ammonia-oxidizing archaea (e.g., Nitrososphaera, 46.8-fold). The β-lactam resistance gene in Thiobacillus and the amoA gene in Nitrososphaera may enhance lincomycin's removal by promoting its hydrolysis and hydroxylation. Overall, this study provides insights into OMP biodegradation mechanisms and the impact of ng/L levels of lincomycin on microbial communities.

Siderophore-Mediated Cooperation in Anammox Consortia

It has been widely accepted that iron plays an important role in stimulating the activity of anammox bacteria, which contain many iron clusters for electron transport in cells. However, whether anammox bacteria could directly use and how to uptake Fe(III) have been long-time ignored. Here, we found that micrometer-scale magnetite with the size of 10-20 μm significantly promoted the anammox bacterial activity by iron core and iron uptake. Anammox bacteria cannot utilize Fe(III) directly as they are unable to secrete siderophore for the extracellular Fe(III) transfer to intracellular. In anaerobic anammox consortia at the presence of magnetite, siderophore synthesis bacteria belonging to Alphaproteobacteria, Candidate phylum, and Chloroflexi secreted abundant siderophores, which combined with Fe(III) ionized from magnetite to form siderophore-Fe(III) complexes. These complexes were then used by anammox bacteria via a specific outer membrane receptor and transported by the transporter protein to the periplasm, further releasing Fe(III). Cytochrome c was then formed by the siderophore-Fe(III) complex reduction, for assimilation and synthesis of Fe-S protein and heme B in anammox bacteria to increase electron transfer capability. This study reveals the siderophore-mediated bacterial cooperation in anammox consortia for Fe(III) assimilation and implies the important role of siderophore-mediated cooperation in driving nitrogen conversion in the artificial or natural system.

FGeneBERT: function-driven pre-trained gene language model for metagenomics

Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.

Habitat-Dependent DNA viral communities in atmospheric aerosols: Insights from terrestrial and marine ecosystems in East Asia

The transmission of viruses through aerosols is of growing public health concern, yet research on aerosol-associated viral communities lags behind that of terrestrial and aquatic ecosystems. Here, DNA viral diversity in natural aerosols from both over land and ocean in the East Asia region was examined. The results showed that atmospheric environments harbor a distinct viral community that differs from those present in terrestrial and aquatic ecosystems. A comparison of aerosol samples from different locations revealed that aerosol viruses are strongly influenced by altitude and their sources. Fragments of viruses that can infect pathogenic bacteria, as well as pathogenic viruses (such as herpesviruses, Inoviruses, and Iridovirus) were detected. Anthropogenically-influenced land aerosol samples contained viral communities with greater richness and diversity as well as a higher relative abundance of pathogenic and lytic viruses compared to pristine marine airborne samples. Furthermore, habitat-specific auxiliary metabolic genes (AMGs) were observed, such as the phosphate regulon (phoH), which was more prevalent in ocean aerosol samples and regulates phosphate uptake under low-phosphate conditions, thereby assisting viral hosts in overcoming metabolic challenges in different environmental conditions. This study highlights the ecological distinctness of the airborne viral community and the interconnectedness between those from land, sea, and atmosphere, underscoring the importance of evaluating their potential pathogenicity in future research.

Deciphering nitrogen removal performance concerning heterotrophic microorganism's succession by using three typical acid-rich fermentation liquids of food waste as carbon sources in high ammonium and high salt wastewater treatment

Understanding the performance and microbial succession in nitrogen removal using fermentation liquid as carbon source can provide a practical basis for treating low C/N ratio wastewater. In this study, three typical fermentation liquids of food waste (FW) enriched with lactic acid (LA), propionic acid (PA), and butyric acid (BA) were added to high ammonia and high salt (HAHS) wastewater treatment process. Results showed that effluent TN decreased from 50 mg/L to around 15 mg/L with the influent concentration around 1000 mg/L after adding fermentation liquid enriched with LA and PA. In contrast, adding BA-rich fermentation liquid gradually deteriorated the nitrogen removal due to the nitrification process being impaired. Genus Thauera predominated in HAHS wastewater system via heterotrophic simultaneous nitrification and denitrification (SND) process. Utilization of LA- and PA-rich fermentation liquids induced the acclimation of other heterotrophic SND microbes and partially replaced Thauera. Conversely, BA-rich carbon source promoted the proliferation of heterotrophic denitrifying and ordinary heterotrophic microorganisms, thereby inhibiting nitrification process and ultimately leading to the failure of nitrogen removal. Meanwhile, the relative abundance of denitrification genes, including napAB, nirKS, norBC, and NosZ, annotated in Thauera exhibited the lowest relative abundance in BA-rich phase. This study provides valuable insights into the mechanism of using FW fermentation liquid as an alternative carbon source to promote nitrogen removal in HAHS wastewater.

Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla

Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, 15N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr-1 (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.

Multi-faceted effects and mechanisms of granular activated carbon to enhance anaerobic ammonium oxidation (anammox) for nitrogen removal from wastewater

Nitrogen removal via anammox is efficient but challenged by their slow growth. Adding granular activated carbon (GAC) increased the total nitrogen removal rate to 66.99 g-N/m3/day, compared to 50.00 g-N/m3/day in non-GAC reactor. Both reactors dominated by Candidatus Brocadia (non-GAC: 36.25 %, GAC: 35.5 %) but GAC improved specific anammox activity. Functional metabolic profiling from metagenomic analysis unveiled that GAC enhanced pathways associated with electron shuttle production, potentially promoting intra/extracellular electron transfer. In nitrogen metabolism, GAC is indicated to facilitate anammox N2H4 synthesis process, and inhibit nitrification and full denitrification processes, functioned by Nitrosomonas and Castellaniella which are more abundant in the non-GAC reactor. GAC also enhanced dissimilatory nitrate reduction to ammonium and partial denitrification processes, providing anammox with NH4+/NO, which was conducted by Anaerolineae members (29.7 % in GAC-reactor and 7.8 % in non-GAC reactor sludge). This research illuminated the intricate microbial nitrogen cycling networks affected by GAC in anammox systems.

Bacterial community composition and metabolic characteristics of three representative marine areas in northern China

Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.

Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system

N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4+-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.

Dominant Dolichospermum and microcystin production in Detroit Lake (Oregon, USA)

The excessive growth of harmful cyanobacteria, including Dolichospermum (formerly known as Anabaena), in freshwater bodies has become a pressing global concern. However, detailed information about the role of Dolichospermum in shaping bloom dynamics and producing cyanotoxins is limited. In this study, a bloom event dominated by Dolichospermum spp. at Detroit Lake (Oregon, USA) was examined from 2019 to 2021. In 2019, early summer cyanobacterial community succession reached up to 8.7 % of total phytoplankton abundance. Dolichospermum was the major microcystin (MC)-producing genus, with peak MC levels of 7.34 μg L-1. The presence of MCs was strongly correlated with the abundance of Dolichospermum (r = 0.84, p < 0.05) and MC synthetase gene, mcyE-Ana (r = 0.63, p < 0.05). Metabolic analyses further showed that the presence of nif/pst genes linked to nitrogen and phosphorus metabolism was dominated by Dolichospermum from the bloom onset until September. In addition, the abundance of Dolichospermum was significantly correlated with the abundance of nitrogen-fixing nif-Ana gene (r = 0.62, p < 0.05). As the lake experienced a longer N and P scarcity period (May to September), the N2-fixing Dolichospermum was able to dominate over other non-fixing cyanobacteria present, including Microcystis and Planktothrix. Overall, our results facilitate a better understanding of the organism and will help working toward managing/predicting future blooms.

How do various strategies for returning residues change microbiota modulation: potential implications for soil health

Introduction

Residue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored.

Methods

In a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK).

Results and discussion

Using metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both α and β) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD < SC < BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes.

γBMGC: A Comprehensive and Accurate Database for Screening TMAO-Associated Cardiovascular Diseases

Dietary l-carnitine produces γ-butylbetaine (γBB) in a gut-microbiota-dependent manner in humans, and has been proven to be an intermediate product possibly associated with incident cardiovascular diseases or major adverse events. Eliminating or reducing the production of microbiota-dependent γBB may contribute to adjuvant therapy for cardiovascular diseases. However, to date, our understanding of the γBB metabolic gene clusters (MGCs) and associated microorganisms remains limited. To solve this problem, we constructed a manually curated γBB metabolic gene cluster database (γBMGC) based on Hidden Markov Models (HMMs). It comprised 171,510 allelic genes from 85 species and 20 genera, which could effectively provide high-resolution analysis at the strain level. For simulated gene datasets, with a 50% identity cutoff, we achieved an annotation accuracy, PPV, specificity, F1-score, and NPV of 99.4%, 97.97%, 99.16%, 98.97%, and 100%, respectively, which significantly outperformed existing databases such as KEGG at similar thresholds. The γBMGC database is more accurate, comprehensive, and faster for profiling cardiovascular disease (CVD)-associated genes at the species or strain level, offering a higher resolution in identifying strain-specific γBB metabolic pathways compared to existing databases like KEGG or COG. Meanwhile, we validated the excellent performance of γBMGC in gene abundance analysis and bacterial species distinction. γBMGC is a powerful database for enhancing our understanding of the microbial l-carnitine pathway in the human gut, enabling rapid and high-accuracy analyses of the associated cardiovascular disease processes.

Deciphering the mechanism of rhizosphere microecosystem in modulating rice cadmium accumulation via integrating metabolomics and metagenomics

Cadmium (Cd) accumulation in rice poses significant risks to human health. The Cd accumulation levels vary widely among cultivars and are strongly associated with the rhizosphere microecosystem. However, the underlying mechanisms remain poorly understood. Here, we conducted a field experiment in Cd-contaminated areas with 24 popular regional cultivars. These cultivars were categorized into high Cd accumulation (HA) and low Cd accumulation (LA) groups based on their grain Cd content. Rhizosphere soil physicochemical properties were monitored, and key metabolites, microbiomes, and their interaction contributing to Cd accumulation were analyzed using omics-sequencing technologies and bioinformatics analysis. Metabolomic analysis identified distinct rhizosphere metabolite profiles between the HA and LA groups, with key metabolites showing strong correlations with Cd accumulation. Key metabolites in the LA group were linked to reduced Cd uptake and enhanced antioxidant defense mechanisms, while those in the HA group were associated with increased Cd mobility and uptake. Metagenomic analysis of the rhizosphere soil showed that the LA group harbored a more diverse and interconnected microbial community, with tax such as Syntrophaceae, Anaerolineae, Thermoflexales, and Syntrophales, along with metabolite such as disopyramide, playing central roles in Cd immobilization and detoxification. Additionally, the enhanced carbon, nitrogen, and phosphorus cycling in the LA group suggests a more robust nutrient assimilation process that supports plant growth and reduces Cd uptake. This study highlights the critical role of the rhizosphere microecosystem in regulating Cd accumulation and underscores the potential of selecting rice cultivars with favorable rhizosphere traits as a strategy for reducing Cd uptake.

Characterization of rhizosphere bacterial communities in oilseed rape cultivars with different susceptibility to Plasmodiophora brassicae infection

Rhizosphere microbiomes are constantly mobilized during plant-pathogen interactions, and this, in turn, affects their interactions. However, few studies have examined the activities of rhizosphere microbiomes in plants with different susceptibilities to soil-borne pathogens, especially those that cause clubroot disease. In this study, we compared the rhizosphere bacterial community in response to infection of Plasmodiophora brassicae among the four different clubroot susceptibility cultivars of oilseed rape (Brassica napus). Our results revealed obvious differences in the responses of rhizosphere bacterial community to the P. brassicae infection between the four cultivars of oilseed rape. Several bacterial genera that are associated with the nitrogen cycle, including Limnobacter, Thiobacillus, Anaeromyxobacter, Nitrosomonas, Tumebacillus, and Halomonas, showed significantly different changes between susceptible and resistant cultivars in the presence of P. brassicae infection. Moreover, increased connectedness and robustness were exhibited in the rhizosphere bacterial community co-occurrence network in clubroot-susceptible cultivars that were infected with P. brassicae, while only slight changes were observed in clubroot-resistant cultivars. Metagenomic analysis of microbial metabolism also indicated differences in the rhizosphere bacterial community between susceptible and resistant cultivars that were infected with P. brassicae. Functional analysis of the nitrogen cycle showed that genes related to nitrification (nxrB) were upregulated in susceptible cultivars, while genes related to assimilatory nitrate reduction (nasA, narB, and nirA) were upregulated in resistant cultivars that were infected with P. brassicae. These findings indicate that the synthesis and assimilation process of NO3 - content were promoted in susceptible and resistant cultivars, respectively. Our study revealed differences in the characteristics of rhizosphere bacterial communities in response to P. brassicae infection between clubroot-susceptible and clubroot-resistant cultivars as well as the potential impact of these differences on the plant-P. brassicae interaction.

Virus-prokaryote interactions assist pollutant removal in constructed wetlands

As a vital part of microbial communities, viruses in constructed wetlands (CWs) remain poorly explored, yet they could significantly affect pollutant removal. Here, two pilot-scale CWs were built to investigate the viral community under different hydraulic loading rates (HLRs) using in-depth metagenomic analysis. Gene-sharing networks suggested that the CWs were pools of unexplored viruses. A higher abundance of prokaryotic functional genes related to sulfur cycling and denitrification was observed in the higher HLR condition, which was associated with greater removal of total nitrogen and nitrate nitrogen compared to the lower HLR condition. Viruses also affect nitrogen pollutant removal by potentially infecting functional prokaryotes, such as denitrification bacteria and ammonia-oxidizing bacteria, and by providing auxiliary metabolic genes involved in sulfur and nitrogen cycling. These findings reveal the significance of viruses in pollutant removal in CWs and enhance the understanding of the relationship between engineering design parameters and performance from microbial perspectives.

Response of ammonium transformation in bioanodes to potential regulation: Performance, electromicrobiome and implications

Understanding how potential regulation affects ammonium transformation in bioanodes is crucial for promoting their application. This study explored the performance, electrochemical properties, electromicrobiome of bioanodes across potentials from 0.0 V to 0.4 V vs. standard hydrogen electrode (SHE). Higher anode potentials enhanced the performance of electroactive biofilms and ammonium removal but suppressed nitrite oxidation while favoring dissimilatory nitrate reduction (DNRA), leading to increased nitrite accumulation. A reduction in nitrite-oxidizing bacteria (NOB) and an increase in DNRA-related genes resulted in an optimal nitrite-to-ammonium ratio of 1.32 for the Anammox process. Higher anodic potentials (0.3 and 0.4 V) were less effective for TN removal than lower potentials (0, 0.1, and 0.2 V), likely due to increased NOB and denitrification genes at lower potentials enhancing nitrite oxidation and denitrification. These findings indicate that regulating anodic potential effectively directs ammonium transformation in bioanodes, optimizing its conversion to N2 or nitrite.

Nitrogen-cycling processes under long-term compound heavy metal(loids) pressure around a gold mine: Stimulation of nitrite reduction

Mining and tailings deposition can cause serious heavy metal(loids) pollution to the surrounding soil environment. Soil microorganisms adapt their metabolism to such conditions, driving alterations in soil function. This study aims to elucidate the response patterns of nitrogen-cycling microorganisms under long-term heavy metal(loids) exposure. The results showed that the diversity and abundance of nitrogen-cycling microorganisms showed negative feedback to heavy metal(loids) concentrations. Denitrifying microorganisms were shown to be the dominant microorganisms with over 60% of relative abundance and a complex community structure including 27 phyla. Further, the key bacterial species in the denitrification process were calculated using a random forest model, where the top three key species (Pseudomonas stutzei, Sphingobium japonicum and Leifsonia rubra) were found to play a prominent role in nitrite reduction. Functional gene analysis and qPCR revealed that nirK, which is involved in nitrite reduction, significantly accumulated in the most metal-rich soil with the increase of absolute abundance of 63.86%. The experimental results confirmed that the activity of nitrite reductase (Nir) encoded by nirK in the soil was increased at high concentrations of heavy metal(loids). Partial least squares-path model identified three potential modes of nitrite reduction processes being stimulated by heavy metal(loids), the most prominent of which contributed to enhanced nirK abundance and soil Nir activity through positive stimulation of key species. The results provide new insights and preliminary evidence on the stimulation of nitrite reduction processes by heavy metal(loids).

The effects of different halogenated-pyrethroid pesticides on soil microbial community

The application of pesticides increases crop yields but affects the structure and function of the soil microbial community. Halogens are common functional modification groups in chemical compounds, and innovative pesticides have been developed on the basis of these groups. However, the effects of different halogen substituents on soil microorganisms remain unclear. This study investigated the effects of three pyrethroid pesticides (deltamethrin, cypermethrin, and cyfluthrin) on the soil microbiota. Our results revealed that all these pesticides significantly reduced the stability of the bacterial communities and decreased bacterial diversity at high concentrations. Compared with deltamethrin (Br-) and cypermethrin (Cl-), low concentrations (0.5 mg/kg) of cyfluthrin (F-) increased soil bacterial diversity by 23.14 % and increased the potential for nitrogen fixation by 2.00 % and nitrification by 3.39 %, thus making it a relatively eco-friendly option. Our findings provide new insights into the potential ecological effects of halogenated pyrethroid pesticides on soil ecosystems.

Diversity and Potential Metabolic Characteristics of Culturable Copiotrophic Bacteria That Can Grow on Low-Nutrient Medium in Zhenbei Seamount in the South China Sea

Oligotrophs are predominant in nutrient-poor environments, but copiotrophic bacteria may tolerate conditions of low energy and can also survive and thrive in these nutrient-limited conditions. In the present study, we isolated 648 strains using a dilution plating method after enrichment for low-nutrient conditions. We collected 150 seawater samples at 21 stations in different parts of the water column at the Zhenbei Seamount in the South China Sea. The 648 isolated copiotrophic strains that could grow on low-nutrient medium were in 21 genera and 42 species. A total of 99.4% (644/648) of the bacteria were in the phylum Pseudomonadota, with 73.3% (472/644) in the class Gammaproteobacteria and 26.7% (172/644) in the class Alphaproteobacteria. Among the 42 representative isolates, Pseudoalteromonas arabiensis, Roseibium aggregatum, and Vibrio neocaledonicus were present in all layers of seawater and at almost all of the stations. Almost half of these species (20/42) contained genes that performed nitrate reduction, with confirmation by nitrate reduction testing. These isolates also contained genes that functioned in sulfur metabolism, including sulfate reduction, thiosulfate oxidation, thiosulfate disproportionation, and dimethylsulfoniopropionate degradation. GH23, CBM50, GT4, GT2, and GT51 were the main carbohydrate-active enzymes (CAZymes), and these five enzymes were present in all or almost all of the isolated strains. The most abundant classes of CAZymes were those associated with the degradation of chitin, starch, and cellulose. Collectively, our study of marine copiotrophic bacteria capable of growing on low-nutrient medium demonstrated the diversity of these species and their potential metabolic characteristics.

Improvement of soil nutrient cycling by dominant plants in natural restoration of heavy metal polluted areas

Referring to the natural succession to restore polluted land is one of the most vital assignments to solving the environmental problems. However, there is little understanding of the natural restoration of nutrient biogeochemical cycles in abandoned land with severe metal pollution. To clarify the nutrient cycling process and the influence of organisms on it, we investigated the magnitude of rhizosphere effects on soil nitrogen (N), phosphorus (P) and sulphur (S) cycles in natural restoration of an abandoned metal mine, as well as the roles of plants and microorganisms in the nutrient cycles. Our data revealed that the rhizosphere had higher levels of ammoniation than non-rhizosphere soil at both stages of restoration. In the early stage, the rhizosphere had greater levels of inorganic phosphorus and organophosphorus solubilisation, as well as sulphite oxidation, compared to non-rhizosphere soil. The bacterial composition influenced the N and S cycles, while the fungal composition had the greatest effect on the P cycles. Furthermore, rhizosphere nutrition cycles and microbial communities altered according plant strategy. Overall, the plants that colonize the early stages of natural recovery demonstrate enhanced restoration of nutrient efficiency. These results contribute to further knowledge of nutrient recovery in mining areas, as well as suggestions for selecting remedial microorganisms and plants in metal-polluted environments.

Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants

The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.

Coupled sulfur and nitrogen cycling at a catchment scale: insights from isotopic and molecular techniques

The biogeochemical cycles of nitrogen (N) and sulfur (S) play important roles in sustaining the Earth's ecosystem. However, their potential coupling process and underlying mechanisms in the nature remain unclear. Through joint applications of river water's isotopic compositions, isotope-pairing experiments, and molecular techniques, this study revealed the coupled N-S cycling processes at a catchment scale from both geochemical and biological perspectives. The river water's natural abundance isotopic compositions indicated that sulfide oxidation was an important source (67.0 ± 5.5 % in summer and 72.0 ± 5.5 % in winter) of riverine sulfate (SO42-). In addition, sulfide oxidation and NOx reduction (especially denitrification) were tightly coupled in summer but less significantly so in winter. However, the coupling of sulfide oxidation and dissimilatory nitrate reduction to ammonium (DNRA) could not be overlooked in winter. The 15N pairing experiments quantitatively showed that the high sulfide oxidation rates in summer (4.7 ± 2.3 mol/km2/h) were significantly associated with the denitrification. Metagenomics and qPCR analyses of the soils supported the isotopic interpretations, substantiating the metabolic potential and coexistence of bacterial denitrification, DNRA, and sulfide oxidation, which was more prevalent in summer. This study reveals comprehensive evidence that sulfide oxidation and NOx reduction are tightly coupled at the catchment scale, which provides a new perspective towards a better understanding of N-S cycling.

Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping

The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.

Investigating drivers of N2 loss and N2O reducers in paddy soils across China

Denitrification plays a pivotal role in nitrogen (N) cycling in rice paddies, significantly impacting N loss and greenhouse gas emissions. Accurate quantification of net N2 emissions from paddy fields is therefore essential for improving fertilizer N use efficiency. However, challenges in directly measuring gaseous N2 hinder our understanding of microbially-mediated N loss in paddy soils at large scales. In this study, we investigated net N2 loss and its influencing factors in 45 paddy soils across China using membrane inlet mass spectrometry and N2/Ar technique, complemented by microbial community analysis via metagenomics. Potential N2 loss rates varied from 0.41 to 3.58 nmol N g-1 h-1, with no significant regional differences. However, soils from rice-upland rotation (1.72 ± 0.64 nmol N g-1 h-1) and mono-rice cropping systems (1.41 ± 0.53 nmol N g-1 h-1) exhibited higher N2 loss rates compared to double-rice cropping soils (1.13 ± 0.62 nmol N g-1 h-1). Our results revealed a unimodal relationship between soil N2 loss rates and soil pH, with N2O reducers and soil properties primarily regulating regional variations in N2 loss. Significant ecological differentiation was observed within both nosZ Clade I and Clade II, with soil pH emerging as the key factor shaping their community composition. Specifically, in rice-upland rotations, soil moisture and pH significantly influenced nosZ Clade I, while in double-rice cropping systems, soil texture and pH were the main factors affecting nosZ Clade II, thereby driving N2 loss. These findings enhance our understanding of N2 loss dynamics in paddy soil ecosystems, underscoring the critical role of N2O reducers on microbial-derived N2 loss and highlighting the importance of developing strategies to mitigate N2O emissions by balancing N2 loss through the manipulation of N2O-reducing and N2O-producing microbes.

Arsenic-induced enhancement of diazotrophic recruitment and nitrogen fixation in Pteris vittata rhizosphere

Heavy metal contamination poses an escalating global challenge to soil ecosystems, with hyperaccumulators playing a crucial role in environmental remediation and resource recovery. The enrichment of diazotrophs and resulting nitrogen accumulation promoted hyperaccumulator growth and facilitated phytoremediation. Nonetheless, the regulatory mechanism of hyperaccumulator biological nitrogen fixation has remained elusive. Here, we report the mechanism by which arsenic regulates biological nitrogen fixation in the arsenic-hyperaccumulator Pteris vittata. Field investigations and greenhouse experiments, based on multi-omics approaches, reveal that elevated arsenic stress induces an enrichment of key diazotrophs, enhances plant nitrogen acquisition, and thus improves plant growth. Metabolomic analysis and microfluidic experiments further demonstrate that the upregulation of specific root metabolites plays a crucial role in recruiting key diazotrophic bacteria. These findings highlight the pivotal role of nitrogen-acquisition mechanisms in the arsenic hyperaccumulation of Pteris vittata, and provide valuable insights into the plant stress resistance.

Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates

Anthropogenic nitrogen (N) inputs substantially influence the N cycle in agricultural ecosystems. However, the potential links among various environmental factors, nitrogen functional genes, and transformation rates under N fertilization remain poorly understood. Here, we conducted a five-year field experiment and collected 54 soil samples from three 0-4 m boreholes across different treatments: control, N-addition (nitrogen fertilizer) and NPK-addition (combined application of nitrogen, phosphorus and potassium fertilizers) treatments. Our results revealed pronounced variations in soil physiochemical parameters, metal concentrations and antibiotic levels under both N and NPK treatments. These alternations induced significant shifts in bacterial and fungal communities, altered NFG abundance and composition, and greatly enhanced rates of nitrate reduction processes. Notably, nutrients, antibiotics and bacteria exerted a more pronounced influence on NFGs and nitrate reduction under N treatment, whereas nutrients, metals, bacteria and fungi had a significant impact under NPK treatment. Furthermore, we established multidimensional correlations between nitrate reduction gene profiles and the activity rates under N and NPK treatments, contrasting with the absence of significant relationships in the control treatment. These findings shed light on the intricate relationships between microbial genetics and ecosystem functions in agricultural ecosystem, which is of significance for predicting and managing metabolic processes effectively.

Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen

Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.

Wastewater treatment plant effluents increase the global warming potential in a subtropical urbanized river

Rivers play a pivotal role in global carbon (C) and nitrogen (N) biogeochemical cycles. Urbanized rivers are significant hotspots of greenhouse gases (GHGs, N2O, CO2 and CH4) emissions. This study examined the GHGs distributions in the Guanxun River, an effluents-receiving subtropical urbanized river, as well as the key environmental factors and processes affecting the pattern and emission characteristics of GHGs. Dissolved N2O, CO2, and CH4 concentrations reached 228.0 nmol L-1, 0.44 mmol L-1, and 5.2 μmol L-1 during the wet period, and 929.8 nmol L-1, 0.7 mmol L-1, and 4.6 μmol L-1 during the dry period, respectively. Effluents inputs increased C and N loadings, reduced C/N ratios, and promoted further methanogenesis and N2O production dominated by incomplete denitrification after the outfall. Increased urbanization in the far downstream, high hydraulic residence time, low DO and high organic C environment promoted methanogenesis. The strong CH4 oxidation and methanogenic reactions inhibited by the effluents combined to suppress CH4 emissions in downstream near the outfall, and the process also contributed to CO2 production. The carbon fixation downstream from the outfall were inhibited by effluents. Ultimately, it promoted CO2 emissions downstream from the outfall. The continuous C, N, and chlorine inputs maintained the high saturation and production potential of GHGs, and altered microbial community structure and functional genes abundance. Ultimately, the global warming potential downstream increased by 186 % and 84 % during wet and dry periods on the 20-year scale, and increased by 91 % and 49 % during wet and dry periods on the 100-year scale, respectively, compared with upstream from the outfall. In urbanized rivers with sufficient C and N source supply from WWTP effluents, the large effluent equivalently transformed the natural water within the channel into a subsequent "reactor". Furthermore, the IPCC recommended EF5r values appear to underestimate the N2O emission potential of urbanized rivers with high pollution loading that receiving WWTP effluents. The findings of this study might aid the development of effective strategies for mitigating global climate change.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BACKGROUND

Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS

Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS

Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.